[biwenzel]

tried csolnp but removed again, since it slowed down out test
added normalization to wrapper, now every dataset has to run through the normaliztaion function before aggregation (error otherwise) (#16)
added protOrigin from fasta to graph (#7)
added tests for summarized results

[Copilot]

Pull request overview

This PR updates the bppg workflow to enforce peptide-intensity normalization before aggregation, and propagates protein-origin metadata (protOrigin) from FASTA/edgelists into generated graphs, with expanded snapshot testing and vignette scaffolding.

Changes:

• Enforce/use normalization in the graph-generation wrapper path and rename expected assay to intensities_norm for downstream aggregation.
• Add protOrigin as a protein-node attribute in graph generation and ensure it survives node contraction.
• Extend snapshot tests for graph generation and aggregated/exported results; add initial vignette + vignette tooling metadata.

Reviewed changes

Copilot reviewed 18 out of 21 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
R/wrapperGraph.R	Adds normalization step to quant wrapper and writes out normalized data.
R/02_peptidePreprocessing.R	Makes aggregateReplicates() require intensities_norm.
R/04_graphGeneration.R	Adds protOrigin vertex attribute and handles it during contraction.
R/06_optimization.R	Adds m == 1 special-case optimization return.
R/03_FASTAPreprocessing.R	Minor warning formatting tweak.
man/generateGraphsFromQuantData.Rd	Documents new norm_method parameter.
man/aggregateReplicates.Rd	Updates argument text to reflect normalized inputs.
man/normalizePeptideIntensities.Rd	(Regenerated) now reflects inherited param text (currently incorrect).
tests/testthat/test_02_peptideProcessing.R	Updates tests to use intensities_norm and snapshots normalized assays.
tests/testthat/test_04_graphGeneration.R	Adds contraction-mapping snapshots and protOrigin attribute assertions.
tests/testthat/test_06_optimization.R	Formatting-only changes.
tests/testthat/test_07_resultAggregation_and_Export.R	Adds snapshots for summarized experiment components.
tests/testthat/test_plotting.R	Minor comment tweak.
tests/testthat/_snaps/*	Updates snapshots due to normalization/attribute changes.
vignettes/bppg.Rmd	Adds vignette skeleton.
vignettes/.gitignore	Ignores built vignette artifacts.
DESCRIPTION	Adds vignette dependencies and VignetteBuilder.
.gitignore	Ignores inst/doc.

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